Conclusions: Arginine, glutamine and glutathione, amino acids known to be involved in cellular stress responses, were increased in retinal neurons and glial cells upon smoke exposure. Eliminating essential components of the complement system, a cascade required for the maintenance of the immune privilege of the eye, appears to exacerbate responses to cigarette smoke in oxidative damage response related pathways. Understanding complement-dependent alterations in the eye will aid in our understanding of AMD pathology and may open new avenues for novel treatment strategies.